[phenixbb] labelit.index python error

[Nicholas Sauter]

Hi,

We found this bug too, and fixed it over the weekend, so the very latest
phenix nightly build should be OK.  The indexing results themselves are not
affected by the bug.

Nick Sauter

On Tue, Jan 31, 2012 at 7:15 AM, Christian Roth <
christian.roth at bbz.uni-leipzig.de> wrote:

> Hi,
>
> I had a few images, some of them are very bad. So itried to index 1 of the
> pictures, and indexing went very well, but then a strange error appeared
> which
> I cannot relate to anything.
> What might be the problem here?
>
> Best Regards
>
> Christian
>
> labelit.index_dev-968
> /hosts/vulcan1/mar345/moschuetz/064c2_4/064c2_4_001.mar2300
>
>
> Beam center is not immediately clear; rigorously retesting 2 solutions
> Beam x 172.5 y 172.9, initial score 405; refined rmsd: 0.1445 <Z>=20.4
> Beam x 171.8 y 175.6, initial score 335; refined rmsd: 0.2160 <Z>=14.9
>
> LABELIT Indexing results:
> Beam center x  172.58mm, y  172.91mm, distance  209.93mm ; 80%
> mosaicity=0.25
> deg.
>
> Solution  Metric fit  rmsd  #spots  crystal_system   unit_cell
> volume
> :)   2     0.2528 dg 0.105    190    monoclinic mC  248.48  71.93 154.76
> 90.00 112.70  90.00  2551913
> :)   1     0.0000 dg 0.076    203     triclinic aP   71.93 129.30 154.76
> 111.69  90.25 106.07  1275944
>
> MOSFLM Integration results:
> Solution  SpaceGroup Beam x   y  distance  Resolution Mosaicity RMS
> :)   2           C2 172.89 172.41  209.92       2.54    0.250000    0.109
>     1           P1 172.88 172.36  209.85       2.37    0.250000    0.094
> show_stack(1): /userdata-2/christian/phenix-
> dev-968/labelit/command_line/screen.py(84) top_level_indexing
> show_stack(2): /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/../../labelit/command_line/index.py(5) <module>
> libc backtrace (28 frames, most recent call last):
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x8058241]
>  /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x4009fb56]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(main+0x17) [0x80582df]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(Py_Main+0xaba) [0x8058f2a]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(PyRun_SimpleFileExFlags+0xb5) [0x80f61fd]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(PyRun_FileExFlags+0xdc) [0x80f52cc]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(PyEval_EvalCode+0x22) [0x80d659e]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x603) [0x80d63f3]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x622e) [0x80d5ad6]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x3dc7) [0x80d366f]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(PyObject_Call+0x46) [0x806162a]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x8147760]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x4ba) [0x80d62aa]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x8145ea2]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x8064f09]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x8089ab0]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x8064f09]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x8089ab0]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x807b94a]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x80a3710]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x8089ab0]
>  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python
> [0x80a3677]
>  /userdata-2/christian/phenix-dev-968/build/intel-
> linux-2.6/lib/libboost_python.so [0x4036b67b]
>  /userdata-2/christian/phenix-dev-968/build/intel-
>
> linux-2.6/lib/cbflib_ext.so(boost::python::objects::value_holder<iotbx::detectors::Mar345Adaptor>::~value_holder()+0x4a)
> [0x42a13f22]
>  /lib/tls/i686/cmov/libc.so.6(fclose+0x1a0) [0x400e4640]
>  /lib/tls/i686/cmov/libc.so.6(fclose+0x41) [0x4018f241]
>  [0x4001d400]
>  /userdata-2/christian/phenix-dev-968/build/intel-
>
> linux-2.6/lib/boost_python_meta_ext.so(boost_adaptbx_segmentation_fault_backtrace+0x1f)
> [0x4032231f]
> Segmentation fault (Python and libc call stacks above)
>                This crash may be due to a problem in any imported
>                Python module, including modules which are not part
>                of the cctbx project. To disable the traps leading
>                to this message, define these environment variables
>                (e.g. assign the value 1):
>                    BOOST_ADAPTBX_FPE_DEFAULT
>                    BOOST_ADAPTBX_SIGNALS_DEFAULT
>                This will NOT solve the problem, just mask it, but
>                may allow you to proceed in case it is not critical.
>
> --
> Christian Roth
> Institut für Bioanalytische Chemie
> Biotechnologisch-Biomedizinisches Zentrum
> Fakultät für Chemie und Mineralogie
> Universität Leipzig
> Deutscher Platz 5
> 04103 Leipzig
> Telefon: +49 (0)341 97 31316
> Fax: +49 (0)341 97 31319
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>



-- 
Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Physical Biosciences Division
Acting Head, Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 64R0121
Berkeley, CA 94720-8118
(510) 486-5713
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